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X-RAY DIFFRACTION
Materials and Methods page
3VQY
  •   Crystallization Hide
    Crystallization Experiments
    Method VAPOR DIFFUSION, HANGING DROP
    pH 7
    Temperature 293.0
    Details Na/Cacodylate, MgCl2, PEG3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
     
  •   Crystal Data Hide
    Unit Cell
    Length    (Å) Angle    (°)
    a = 103.36 α = 90
    b = 103.36 β = 90
    c = 70.91 γ = 120
     
    Space Group
    Space Group Name:    P 64
     
     
  •   Diffraction Hide
    Diffraction Experiment
    Diffrn ID 1
    Data Collection Temperature 100
     
    Diffraction Detector
    Detector CCD
    Type ADSC QUANTUM 210
    Collection Date 2004-11-16
     
    Diffraction Radiation
    Diffraction Protocol SINGLE WAVELENGTH
     
    Diffraction Source
    Source SYNCHROTRON
    Type PHOTON FACTORY BEAMLINE AR-NW12A
    Wavelength List 1.0000
    Site PHOTON FACTORY
    Beamline AR-NW12A
     
     
  •   Refinement Data Hide
    Reflection Details
    Resolution(High) 2.4
    Resolution(Low) 50
    Number Reflections(Observed) 16537
    Percent Possible(Observed) 97.2
    B(Isotropic) From Wilson Plot 36.9
    Redundancy 6.7
     
    High Resolution Shell Details
    Resolution(High) 2.4
    Resolution(Low) 2.44
    Percent Possible(All) 92.5
    R-Sym I(Observed) 0.247
    Redundancy 3.4
     
     
  •   Refinement Hide
    Refinement Statistics
    Structure Solution Method MOLECULAR REPLACEMENT
    reflnsShellList 2.4
    Resolution(Low) 41.76
    Cut-off Sigma(F) 0.0
    Number of Reflections(Observed) 16530
    Number of Reflections(R-Free) 1661
    Percent Reflections(Observed) 97.3
    R-Factor(Observed) 0.197
    R-Work 0.197
    R-Free 0.231
    R-Free Selection Details RANDOM
     
    Temperature Factor Modeling
    Isotropic Thermal Model RESTRAINED
    Mean Isotropic B Value 45.8
    Anisotropic B[1][1] -7.04
    Anisotropic B[1][2] 3.54
    Anisotropic B[1][3] 0.0
    Anisotropic B[2][2] -7.04
    Anisotropic B[2][3] 0.0
    Anisotropic B[3][3] 14.08
     
    Resolution Shells
    Refinement method X-RAY DIFFRACTION
    Shell Resolution(High) 2.4
    Shell Resolution(Low) 2.55
    Number of Reflections(R-Free) 259
    Number of Reflections(R-Work) 2319
    R-Factor(R-Work) 0.258
    R-Factor(R-Free) 0.268
    R-Free Error 0.017
    Percent Reflections(Observed) 92.1
     
    RMS Deviations
    Parameter Type Deviation from Ideal
    c_scangle_it 3.61
    c_scbond_it 2.37
    c_mcangle_it 2.45
    c_mcbond_it 1.42
    c_improper_angle_d 1.77
    c_dihedral_angle_d 23.1
    c_angle_deg 1.4
    c_bond_d 0.007
     
    Coordinate Error
    Luzzati ESD(Observed) 0.26
    Luzzati Sigma A(Observed) 0.31
    Luzzati Resolution Cutoff(Low) 5.0
    Luzzati ESD(R-Free Set) 0.32
    Luzzati Sigma A(R-Free Set) 0.35
     
    Number of Non-Hydrogen Atoms Used in Refinement
    Protein Atoms 2087
    Nucleic Acid Atoms 0
    Heterogen Atoms 50
    Solvent Atoms 98
     
     
  •   Software and Computing Hide
    Computing
    Data Collection HKL-2000
    Data Reduction (intensity integration) DENZO
    Data Reduction (data scaling) SCALEPACK
    Structure Solution MOLREP
    Structure Refinement CNS 1.1
     
    Software
    refinement CNS version: 1.1
    model building MOLREP
    data collection HKL-2000